java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmWatershed

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmWatershed
extends AlgorithmBase
```
This program applies the watershed algorithm to the image. It assumes that the user has identified the starting watershed regions via VOIs. Future work might be to develop a algorithm that automatically identifies initial seed points and regions or possibly an automatic method that forms watersheds - see method at end of file (does not work yet);

Version:

1.1 March 11, 1998

Author:

Matthew J. McAuliffe, Ph.D. and Ray Lert, MD

Nested Class Summary

Nested Classes
Modifier and Type Class Description

private class AlgorithmWatershed.Seed
Simple class to hold seed point and basin (object label) value.
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private static short`	`BOUNDARY`	DOCUMENT ME!
`private ModelImage`	`energyImage`	DOCUMENT ME!
`private boolean`	`entireImage`	If true, ignore VOIs and process entire image
`private static short`	`INITIAL`	DOCUMENT ME!
`private static short`	`MASK`	DOCUMENT ME!
`private java.util.Vector<AlgorithmWatershed.Seed>`	`seedVector`	DOCUMENT ME!
`private float[]`	`sigmas`	DOCUMENT ME!
`private static short`	`WSHED`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmWatershed(ModelImage destImg, ModelImage srcImg, ModelImage gmImg, float[] sigmas, java.util.Vector<AlgorithmWatershed.Seed> seeds)`	Constructs new watershed algorithm.
`AlgorithmWatershed(ModelImage destImg, ModelImage srcImg, ModelImage gmImg, float[] sigmas, java.util.Vector<AlgorithmWatershed.Seed> seeds, boolean entireImage)`	Constructs new watershed algorithm.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calc2D()`	Calculates the watershed intialized by the VOI regions.
`private void`	`calc3D()`	Calculates the watershed intialized by the VOI regions.
`void`	`finalize()`	Prepares this class for destruction.
`void`	`runAlgorithm()`	Starts the program.
`void`	`setEnergyImage(ModelImage _energyImage)`	This image is typically the gradient magnitude.
`void`	`setSeedVector(WildMagic.LibFoundation.Mathematics.Vector3f[] seedPoints)`	Sets the seed vector.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - BOUNDARY
```
private static final short BOUNDARY
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MASK
```
private static final short MASK
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - INITIAL
```
private static final short INITIAL
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - WSHED
```
private static final short WSHED
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - energyImage
```
private ModelImage energyImage
```
    DOCUMENT ME!
  - seedVector
```
private java.util.Vector<AlgorithmWatershed.Seed> seedVector
```
    DOCUMENT ME!
  - sigmas
```
private float[] sigmas
```
    DOCUMENT ME!
  - entireImage
```
private boolean entireImage
```
    If true, ignore VOIs and process entire image
- Constructor Detail
  - AlgorithmWatershed
```
public AlgorithmWatershed(ModelImage destImg,
                          ModelImage srcImg,
                          ModelImage gmImg,
                          float[] sigmas,
                          java.util.Vector<AlgorithmWatershed.Seed> seeds)
```
    Constructs new watershed algorithm.
    
    Parameters:
    
    destImg - Image model where result image is to stored
    
    srcImg - Source image model
    
    gmImg - Gradient magnitude image (can be null)
    
    sigmas - Gaussian's standard deviations in the each dimension
    
    seeds - Seed points for starting watershed
  - AlgorithmWatershed
```
public AlgorithmWatershed(ModelImage destImg,
                          ModelImage srcImg,
                          ModelImage gmImg,
                          float[] sigmas,
                          java.util.Vector<AlgorithmWatershed.Seed> seeds,
                          boolean entireImage)
```
    Constructs new watershed algorithm.
    
    Parameters:
    
    destImg - Image model where result image is to stored
    
    srcImg - Source image model
    
    gmImg - Gradient magnitude image (can be null)
    
    sigmas - Gaussian's standard deviations in the each dimension
    
    seeds - Seed points for starting watershed
    
    entireImage - If true, ignore VOIs and process entire image
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - setEnergyImage
```
public void setEnergyImage(ModelImage _energyImage)
```
    This image is typically the gradient magnitude. Peaks in this image (function ) are the watersheds boundaries
    
    Parameters:
    
    _energyImage - the energy image (function)
  - setSeedVector
```
public void setSeedVector(WildMagic.LibFoundation.Mathematics.Vector3f[] seedPoints)
```
    Sets the seed vector.
    
    Parameters:
    
    seedPoints - The seed points.
  - calc2D
```
private void calc2D()
```
    Calculates the watershed intialized by the VOI regions. The resultant watershed regions(basin) are labelled with an integer value. In addition, each region is separated by connected (8-way) watershed identifier of 1.
  - calc3D
```
private void calc3D()
```
    Calculates the watershed intialized by the VOI regions. The resultant watershed regions(basin) are labelled with an integer value. In addition, each region is separated by connected (8-way) watershed identifier of 1.

Class AlgorithmWatershed

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

BOUNDARY

MASK

INITIAL

WSHED

energyImage

seedVector

sigmas

entireImage

Constructor Detail

AlgorithmWatershed

AlgorithmWatershed

Method Detail

finalize

runAlgorithm

setEnergyImage

setSeedVector

calc2D

calc3D